DEanalysis_kfish_osmotic

Global parameters for modeling

Loading required package: MASS
Loading required package: ggplot2
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Loading required package: cowplot

Attaching package: ‘cowplot’

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The following objects are masked from ‘package:GenomicRanges’:

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Attaching package: ‘tidyr’

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Loading required package: ggrepel

R version 3.5.2 (2018-12-20)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS High Sierra 10.13.3

Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats4    parallel  stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] ggrepel_0.8.0               tidyr_0.8.3                 dplyr_0.8.0.1               cowplot_0.9.4              
 [5] pheatmap_1.0.12             gtools_3.8.1                ggplot2_3.1.1               MASS_7.3-51.4              
 [9] DESeq2_1.22.2               SummarizedExperiment_1.12.0 DelayedArray_0.8.0          BiocParallel_1.16.6        
[13] matrixStats_0.54.0          GenomicRanges_1.34.0        GenomeInfoDb_1.18.2         IRanges_2.16.0             
[17] S4Vectors_0.20.1            vsn_3.50.0                  Biobase_2.42.0              BiocGenerics_0.28.0        
[21] lattice_0.20-38             gplots_3.0.1.1              RColorBrewer_1.1-2          edgeR_3.24.3               
[25] limma_3.38.3               

loaded via a namespace (and not attached):
 [1] bitops_1.0-6           bit64_0.9-7            tools_3.5.2            backports_1.1.4       
 [5] R6_2.4.0               affyio_1.52.0          rpart_4.1-13           KernSmooth_2.23-15    
 [9] Hmisc_4.2-0            DBI_1.0.0              lazyeval_0.2.2         colorspace_1.4-1      
[13] nnet_7.3-12            withr_2.1.2            tidyselect_0.2.5       gridExtra_2.3         
[17] bit_1.1-14             compiler_3.5.2         preprocessCore_1.44.0  htmlTable_1.13.1      
[21] caTools_1.17.1.2       scales_1.0.0           checkmate_1.9.1        genefilter_1.64.0     
[25] affy_1.60.0            stringr_1.4.0          digest_0.6.18          foreign_0.8-71        
[29] rmarkdown_1.12         XVector_0.22.0         base64enc_0.1-3        pkgconfig_2.0.2       
[33] htmltools_0.3.6        htmlwidgets_1.3        rlang_0.3.4            rstudioapi_0.10       
[37] RSQLite_2.1.1          jsonlite_1.6           acepack_1.4.1          RCurl_1.95-4.12       
[41] magrittr_1.5           GenomeInfoDbData_1.2.0 Formula_1.2-3          Matrix_1.2-17         
[45] Rcpp_1.0.1             munsell_0.5.0          stringi_1.4.3          yaml_2.2.0            
[49] zlibbioc_1.28.0        plyr_1.8.4             grid_3.5.2             blob_1.1.1            
[53] gdata_2.18.0           crayon_1.3.4           splines_3.5.2          annotate_1.60.1       
[57] locfit_1.5-9.1         knitr_1.22             pillar_1.3.1           geneplotter_1.60.0    
[61] XML_3.98-1.19          glue_1.3.1             evaluate_0.13          latticeExtra_0.6-28   
[65] data.table_1.12.2      BiocManager_1.30.4     gtable_0.3.0           purrr_0.3.2           
[69] assertthat_0.2.1       xfun_0.6               xtable_1.8-3           rsconnect_0.8.13      
[73] survival_2.44-1.1      tibble_2.1.1           AnnotationDbi_1.44.0   memoise_1.1.0         
[77] cluster_2.0.8          statmod_1.4.30        

Number of raw counts, samples

 [1] "physiologyFW"                            "physiologyM"                            
 [3] "condition15_ppt"                         "cladeClade2"                            
 [5] "cladeClade3"                             "physiologyM:condition15_ppt"            
 [7] "physiologyM:cladeClade2"                 "physiologyM:cladeClade3"                
 [9] "condition15_ppt:cladeClade2"             "condition15_ppt:cladeClade3"            
[11] "physiologyM:condition15_ppt:cladeClade2" "physiologyM:condition15_ppt:cladeClade3"
[1] 12
attr(,"method")
[1] "tolNorm2"
attr(,"useGrad")
[1] FALSE
attr(,"tol")
[1] 1.798561e-14
[1] 81 12

[1] 0.751381

Exploratory Plots

Heatmaps

Individuals clustered by overall expression

Individuals by Top 100 genes heatmap

Individuals clustered by top 100 gene expression

PCA for overall expression